A Method for Tracking CRISPR/Plasmidome Dynamics in Complex Bacterial Communities

• Applicants: Professorin Dr. Alice C. McHardy; Professorin Dr. Barbara Stecher-Letsch
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2016 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 315980449

The rising prevalence of antibiotic-resistant (ABR) human pathogens is a major threat to public health. Current strategies to interfere with transmission of ABRs, including antibiotic stewardship and increased hygiene, seem to be insufficient to prevent the emergence and spread of ABR pathogens, resulting in an urgent need to develop novel strategies. Recent studies have highlighted the role of the bacterial adaptive immune system (Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (cas) genes in naturally preventing horizontal gene transfer (HGT) in ABR pathogens. All currently available bioinformatic tools that aim to identify the CRISPR loci or resistance genes in bacterial genomes are insufficient, particularly for application on metagenomic datasets. We therefore propose to establish a computational framework to identify and characterize CRISPR spacer sequences within metagenomic datasets (Objective 1) as well as for the reconstruction of plasmids (Objective 2). Using this framework, we plan to characterize the CRISPR spacer regions in metagenomics datasets of antibiotic-treated mice on a temporal scale, with respect to their ABR gene content (Objective 3). Furthermore, we plan to test the hypothesis that CRISPR interference can naturally target ABR elements and thereby limit HGT of ABR genes. To this end, we will use a mouse model harboring a defined microbial community of sequenced bacterial strains with a known ABR and CRISPR spacer pool. Mice will be challenged with different antibiotics (e.g. selecting for ABRs present in the community) and HGT of ABRs as well as CRISPR system evolution in the bacterial community will be analyzed (Objective 4). In conclusion, the tools developed in this project will help to further clarifying the role of the CRISPR system in preventing the spread of ABRs. This will eventually open up new ways to develop strategies to counteract the emergence of new ABR pathogens.

• DFG Programme: Research Grants